CPT 81286 FXN Gene Sequencing Reimbursement | OpenPayer

Summary & Overview

CPT 81286: Full Sequencing of the Frataxin (FXN) Gene

CPT code 81286 represents full-gene sequencing of the frataxin gene (FXN), a molecular diagnostic test used to detect sequence variants associated with conditions such as Friedreich ataxia. Nationally, comprehensive gene sequencing codes like this are important for accurate genetic diagnosis, informing clinical management, family counseling, and eligibility for targeted therapies or trials. Payers commonly involved in coverage decisions include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare.

This publication provides a concise overview of CPT code 81286: its clinical context, typical sites of service, and the role of full-gene FXN sequencing in diagnosis. Readers will find benchmarks and practical information relevant to billing and claims handling, a summary of common modifiers and testing context, and notes on clinical utility and reporting expectations. The report highlights payer coverage patterns and policy considerations at a national level, as well as operational details labs and billing staff need to process claims using this code.

Data not available in the input for associated taxonomies, specific ICD-10 diagnoses, and related codes.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicareCPT 81286frataxinFXN genegenetic testingmolecular diagnosticsfull gene sequencinglaboratory billinggenetics billing

Billing Code Overview

CPT code 81286 describes a laboratory service that analyzes the full coding sequence of the frataxin gene (FXN). The procedure involves laboratory-based molecular testing to determine the nucleotide sequence across the entire FXN gene to identify pathogenic variants associated with disorders such as Friedreich ataxia.

Service Type: Genetic sequencing / molecular diagnostic test

Typical Site of Service: Clinical laboratory / reference molecular diagnostics laboratory

Data not available in the input.

Clinical & Coding Specifications

Clinical Context

A typical patient is an adult with progressive gait instability, limb weakness, sensory loss, or a family history suggestive of hereditary ataxia. A neurologist or genetic counselor orders full-sequence analysis of the frataxin gene (FXN) to evaluate for Friedreich ataxia when clinical signs (ataxia, dysarthria, loss of proprioception) and supportive tests (absent or reduced deep tendon reflexes, spinal cord atrophy on MRI, or abnormal nerve conduction studies) raise suspicion. The workflow begins with outpatient consultation and informed consent, blood specimen collection (EDTA tube) sent to a molecular diagnostics laboratory, technologist and molecular analyst performing DNA extraction, PCR and/or next-generation sequencing covering the entire FXN coding region and relevant intronic regions, interpretation of sequence variants, and a lab report that includes variant classification per ACMG guidelines. Results are reviewed by the ordering provider and genetic counseling is offered for positive, uncertain, or carrier findings. Typical site of service is an ambulatory clinic for specimen collection with testing performed at a reference molecular genetics laboratory. Service type: clinical molecular diagnostic laboratory test (full gene sequence analysis).

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	When billing separates the professional interpretation from the technical lab work and the provider bills for interpretation.

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Taxonomy Code	Specialty	Notes
207RG0300X	Neurology	Ordering providers who evaluate ataxia and coordinate testing.
207K00000X	Clinical Geneticist	Specialists who diagnose hereditary ataxias and interpret genetic results.
363L00000X	Laboratory - Molecular Pathology	Laboratories and directors performing sequencing and interpretation.
2080P0207X	Genetic Counseling	Providers who perform pre- and post-test counseling related to FXN testing.
208D00000X	Clinical Laboratory	Facilities that collect specimens and send to molecular reference labs.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`G11.1`	Early-onset cerebellar ataxia	Friedreich ataxia commonly presents as progressive cerebellar ataxia; sequencing FXN is relevant for diagnosis.
`G11.4`	Hereditary spastic paraplegia	Overlap in hereditary neurologic presentations where FXN testing may be considered in differential diagnosis.
`G60.9`	Hereditary and idiopathic neuropathy, unspecified	Peripheral neuropathy is part of Friedreich ataxia phenotype; supports genetic testing.
`R26.0`	Ataxic gait	A presenting sign prompting FXN genetic analysis.
`R47.1`	Dysarthria and anarthria	Speech disturbance common in spinocerebellar and Friedreich ataxia; supports ordering FXN testing.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81286`	Analysis of the entire coding sequence of the frataxin gene (FXN)	Primary procedure: full-gene sequencing to detect point variants and small indels in FXN.
`81292`	Detection of GAA repeat expansions in the frataxin (FXN) gene	Complementary test often required because Friedreich ataxia is commonly caused by GAA trinucleotide repeat expansions not always detected by sequencing; may be performed before or alongside `81286`.
`81479`	Unlisted molecular pathology procedure	Used when a novel or nonstandard molecular analysis related to FXN is required and no specific code applies.
`81162`	CPT for targeted genomic sequence analysis (example)	May be used when a specific variant analysis or targeted assay for known FXN variants is performed instead of full sequencing.
`80500`	From a molecular laboratory series (example)	Laboratory workflow codes for technical processes (used by some payers/labs in mapping technical activities); relates to specimen handling and sequencing run overhead.

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